Bottom Line:
Genome-wide estimates were compared with those obtained from microsatellite and from pedigree data.However, estimates of effective population size obtained from changes in coancestry or inbreeding differed.Our results indicate that genome-wide information represents a useful alternative to genealogical information for measuring and maintaining genetic diversity.

ABSTRACTMaintaining genetic variation and controlling the increase in inbreeding are crucial requirements in animal conservation programs. The most widely accepted strategy for achieving these objectives is to maximize the effective population size by minimizing the global coancestry obtained from a particular pedigree. However, for most natural or captive populations genealogical information is absent. In this situation, microsatellites have been traditionally the markers of choice to characterize genetic variation, and several estimators of genealogical coefficients have been developed using marker data, with unsatisfactory results. The development of high-throughput genotyping techniques states the necessity of reviewing the paradigm that genealogical coancestry is the best parameter for measuring genetic diversity. In this study, the Illumina PorcineSNP60 BeadChip was used to obtain genome-wide estimates of rates of coancestry and inbreeding and effective population size for an ancient strain of Iberian pigs that is now in serious danger of extinction and for which very accurate genealogical information is available (the Guadyerbas strain). Genome-wide estimates were compared with those obtained from microsatellite and from pedigree data. Estimates of coancestry and inbreeding computed from the SNP chip were strongly correlated with genealogical estimates and these correlations were substantially higher than those between microsatellite and genealogical coefficients. Also, molecular coancestry computed from SNP information was a better predictor of genealogical coancestry than coancestry computed from microsatellites. Rates of change in coancestry and inbreeding and effective population size estimated from molecular data were very similar to those estimated from genealogical data. However, estimates of effective population size obtained from changes in coancestry or inbreeding differed. Our results indicate that genome-wide information represents a useful alternative to genealogical information for measuring and maintaining genetic diversity.

pone-0078314-g003: Predictions of SNP-based and microsatellite-based molecular coancestry (fM) and genealogical coancestry (fG).(A) Prediction of SNP-based and microsatellite-based molecular coancestry from genealogical coancestry. (B) Prediction of genealogical coancestry from both types of molecular coancestry. The dataset included only the 30 individuals with SNP and microsatellite genotypes available. The complete pedigree information was used for the estimation of genealogical coefficients. Regression equations refer to pairwise coancestries, excluding self-coancestries.

Mentions:
In the group of animals for which microsatellite genotypes were also available, the correlation between genealogical and molecular coancestry (excluding self-coancestries) was substantially higher when the latter was calculated using the SNP chip (0.86) than when calculated using microsatellites (0.67). The correlation between both molecular estimates was as high as 0.86. The prediction of genealogical coancestry from SNPs was more accurate (slope = 0.68, R2 = 0.76) than that from microsatellites (slope = 0.40, R2 = 0.47). As it was observed from the analysis using the whole dataset, the prediction of molecular coancestry from genealogical coancestry was more precise than the prediction of genealogical coancestry from molecular coancestry (Figure 3). Average molecular estimates of coancestry and inbreeding were much lower when using microsatellites than when using SNPs (Table 3). The variance of these estimates were very low (Table 3), ranging from 0.0001 (molecular SNP-based F) to 0.006 (genealogical f).

pone-0078314-g003: Predictions of SNP-based and microsatellite-based molecular coancestry (fM) and genealogical coancestry (fG).(A) Prediction of SNP-based and microsatellite-based molecular coancestry from genealogical coancestry. (B) Prediction of genealogical coancestry from both types of molecular coancestry. The dataset included only the 30 individuals with SNP and microsatellite genotypes available. The complete pedigree information was used for the estimation of genealogical coefficients. Regression equations refer to pairwise coancestries, excluding self-coancestries.

Mentions:
In the group of animals for which microsatellite genotypes were also available, the correlation between genealogical and molecular coancestry (excluding self-coancestries) was substantially higher when the latter was calculated using the SNP chip (0.86) than when calculated using microsatellites (0.67). The correlation between both molecular estimates was as high as 0.86. The prediction of genealogical coancestry from SNPs was more accurate (slope = 0.68, R2 = 0.76) than that from microsatellites (slope = 0.40, R2 = 0.47). As it was observed from the analysis using the whole dataset, the prediction of molecular coancestry from genealogical coancestry was more precise than the prediction of genealogical coancestry from molecular coancestry (Figure 3). Average molecular estimates of coancestry and inbreeding were much lower when using microsatellites than when using SNPs (Table 3). The variance of these estimates were very low (Table 3), ranging from 0.0001 (molecular SNP-based F) to 0.006 (genealogical f).

Bottom Line:
Genome-wide estimates were compared with those obtained from microsatellite and from pedigree data.However, estimates of effective population size obtained from changes in coancestry or inbreeding differed.Our results indicate that genome-wide information represents a useful alternative to genealogical information for measuring and maintaining genetic diversity.

ABSTRACTMaintaining genetic variation and controlling the increase in inbreeding are crucial requirements in animal conservation programs. The most widely accepted strategy for achieving these objectives is to maximize the effective population size by minimizing the global coancestry obtained from a particular pedigree. However, for most natural or captive populations genealogical information is absent. In this situation, microsatellites have been traditionally the markers of choice to characterize genetic variation, and several estimators of genealogical coefficients have been developed using marker data, with unsatisfactory results. The development of high-throughput genotyping techniques states the necessity of reviewing the paradigm that genealogical coancestry is the best parameter for measuring genetic diversity. In this study, the Illumina PorcineSNP60 BeadChip was used to obtain genome-wide estimates of rates of coancestry and inbreeding and effective population size for an ancient strain of Iberian pigs that is now in serious danger of extinction and for which very accurate genealogical information is available (the Guadyerbas strain). Genome-wide estimates were compared with those obtained from microsatellite and from pedigree data. Estimates of coancestry and inbreeding computed from the SNP chip were strongly correlated with genealogical estimates and these correlations were substantially higher than those between microsatellite and genealogical coefficients. Also, molecular coancestry computed from SNP information was a better predictor of genealogical coancestry than coancestry computed from microsatellites. Rates of change in coancestry and inbreeding and effective population size estimated from molecular data were very similar to those estimated from genealogical data. However, estimates of effective population size obtained from changes in coancestry or inbreeding differed. Our results indicate that genome-wide information represents a useful alternative to genealogical information for measuring and maintaining genetic diversity.